Copy and paste the Civ2Unlimited.dll and Civ2Unlimited.exe into your main Test of Time folder (the one with the civ2.exe in it).  

Civ2 Unlimited will not overwrite any of the files in your main folder, it is just a tool to increase some of the ToT limits such as the maximum number of units.

Before you play make sure you have run the FORTRESS.bat batch file. To launch the game double click on the Civ2Unlimited.exe. This will open up a small window with a list of options. Pick:

Game - Test of Time 1.1 [Forced]

Global Game Options - World Max Units: 32,000 

Then hit "Launch Game". Test of Time will then load as normal. Chose to begin or load scenario and find the Fortress Europe scenario file or your save game.

Remember to launch via Civ2Unlimited.exe every time you play Fortress Europe.

If you encounter any problems please ask at the Scenario League Forum where I can usually be found: 

http://apolyton.net/forums/forumdisplay.php?s=&forumid=29